Starting phenix.real_space_refine on Sat Aug 8 14:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2026/8b0j_15785.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 160 5.49 5 S 17 5.16 5 C 9573 2.51 5 N 2853 2.21 5 O 3599 1.98 5 H 12434 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28636 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 3695 Classifications: {'peptide': 268} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 11, 'ASP:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'HIS:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 3571 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 10, 'GLU:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 3462 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 18, 'PHE:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 6, 'HIS:plan': 4, 'GLU:plan': 8, 'TYR:plan': 3, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 3239 Classifications: {'peptide': 266} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 12, 'ASP:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 2, 'HIS:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 259 Chain: "L" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 5605 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 20, 'TRANS': 460} Chain breaks: 3 Unresolved non-hydrogen bonds: 771 Unresolved non-hydrogen angles: 964 Unresolved non-hydrogen dihedrals: 641 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 28, 'ARG:plan': 32, 'ASP:plan': 11, 'TYR:plan': 7, 'HIS:plan': 10, 'ASN:plan1': 6, 'PHE:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 516 Chain: "N" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 4220 Classifications: {'peptide': 356} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 343} Chain breaks: 7 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 11, 'GLN:plan1': 10, 'TYR:plan': 5, 'GLU:plan': 18, 'HIS:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 376 Chain: "K" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 4844 Unexpected atoms: {' U%rna3p_pyr,HO3'': 1} Classifications: {'RNAv2': 160} Modifications used: {'rna2p_pur': 22, 'rna2p_pyr': 23, 'rna3p_pur': 49, 'rna3p_pyr': 66} Link IDs: {'rna2p': 45, 'rna3p': 114} Chain breaks: 6 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 28630 HO3' U K 207 .*. H " Time building chain proxies: 5.19, per 1000 atoms: 0.18 Number of scatterers: 28636 At special positions: 0 Unit cell: (127.14, 131.052, 180.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 160 15.00 O 3599 8.00 N 2853 7.00 C 9573 6.00 H 12434 1.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.